Fish community structure is affected by a range of lake characteristics, including the cover of macrophytes that provide spawning habitats, nursery area, refuge against predators, and food. We assessed fish–macrophyte relationships at both lake and point scale using an extensive dataset from 88 Danish shallow lakes (maximum depth ≤4.5 m). At lake scale, we used mean values from fish and macrophyte community samples for all lakes, in total 88 samples. The point scale data were derived from multiple points in each lake (in total 595 samples) where both macrophytes and fish were sampled, allowing us to assess within-lake variations. We found generally negative relationships between macrophyte cover and fish abundance and biomass, which was strongest at point scale. Contrary to macrophytes, chlorophyll a showed positive relationships with fish abundance—except for perch and all fish <10 cm, which did not show significant relationships. The deeper and more eutrophic the lakes, the more the fish tended to occupy points covered by macrophytes. The abundances of species such as roach and bream were negatively related to macrophyte cover, but, for perch, this relationship was not significant. Our results suggest that fish abundance and biomass were associated with a combination of factors that are often intercorrelated and difficult to isolate. The relationship between fish abundance and biomass and macrophyte cover may depend on, among other factors, fish species, fish size, and the characteristics of the individual lakes.